Use included file for database connection parameters

[atombaby]

The current mechanism puts the database connection string (including username and password) in the process stack where it is viewable by anyone on the system. This is somewhat undesirable- though I don't know precisely what harm could come, general "best practices" would suggest we improve this.

I've done a little work and it looks like we may be able to specify database connection parameters in a file separate from the general Cromwell config (e.g. fh-slurm-sing-cromwell.conf) and use HOCON's include directive:

include required(classpath("application"))
include required(file("database.conf"))
###### FH Slurm Backend, with call caching, without docker/singularity
   ....

Where database.conf contains the database section as specified by Cromwell:

database {
  profile = "slick.jdbc.MySQLProfile$"
  db {
    driver = "com.mysql.cj.jdbc.Driver"
    url = "jdbc:mysql://mydb:32222/cromdb?rewriteBatchedStatements=true&serverTimezone=UTC"
    user = "username"
    password = "password"
    connectionTimeout = 5000
  }
}

The path above doesn't have to be in the current directory- my understanding is that we could specify any path for that, though I'm not sure if things like "~" are expanded.

[vortexing]

This makes things a bit more awkward and requires people to customize more in the way that I'm looking at this now. I need to figure out how to pass the path to the database.conf to the java command so it knows where to look for it in cromServer.sh. If I could figure that out, then it'd be awesome and totally doable.

[vortexing]

@atombaby in the current setup, is this still the case? I've made a lot of changes since then and I'm not sure it's still an issue.